2.0 2012-05-31 14:20:55 -0600 2015-09-17 15:41:47 -0600 ECMDB12185 M2MDB000826 Adenosylcobinamide-GDP Adenosylcobinamide-GDP,a known de novo intermediate, is involved in Porphyrin and chlorophyll metabolism.In Salmonella typhimurium LT2, under anaerobic conditions, CobU (EC 2.7.7.62 and EC 2.7.1.156), CobT (EC 2.4.2.21), CobC (EC 3.1.3.73) and CobS (EC 2.7.8.26) catalyse reactions in the nucleotide loop Adenosine-GDP-cobinamide C68H97CoN21O21P2 1665.5066 1664.597512489 (3R,4S,5S,9S,10S,15S,19R,20R,21R)-19-(2-{[(2R)-2-({[({[(2R,3S,4R,5R)-5-(2-amino-6-oxo-6,9-dihydro-1H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)propyl]carbamoyl}ethyl)-1-{[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl}-5,10,15-tris(2-carbamoylethyl)-4,9,20-tris(carbamoylmethyl)-3,4,7,9,14,14,17,19-octamethyl-2lambda5,22,23lambda5,24lambda5-tetraaza-1-cobaltaoctacyclo[11.9.1.1^{1,8}.0^{2,6}.0^{3,21}.0^{16,23}.0^{18,22}.0^{11,24}]tetracosa-2(6),7,11(24),12,16(23),17-hexaene-2,23,24-tris(ylium)-1,1-diuide (3R,4S,5S,9S,10S,15S,19R,20R,21R)-19-(2-{[(2R)-2-[({[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]propyl]carbamoyl}ethyl)-1-{[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl}-5,10,15-tris(2-carbamoylethyl)-4,9,20-tris(carbamoylmethyl)-3,4,7,9,14,14,17,19-octamethyl-2lambda5,22,23lambda5,24lambda5-tetraaza-1-cobaltaoctacyclo[11.9.1.1^{1,8}.0^{2,6}.0^{3,21}.0^{16,23}.0^{18,22}.0^{11,24}]tetracosa-2(6),7,11(24),12,16(23),17-hexaene-2,23,24-tris(ylium)-1,1-diuide CC(CNC(=O)CC[C@]1(C)[C@@H](CC(N)=O)C2N=C1\C(C)=C1/N=C(/C=C3\N=C(\C(\C)=C4\[C@@H](CCC(N)=O)[C@](C)(CC(N)=O)[C@@]2(C)N4[Co+]C[C@H]2O[C@H]([C@H](O)[C@@H]2O)N2C=NC4=C2N=CN=C4N)[C@@](C)(CC(N)=O)[C@@H]3CCC(N)=O)C(C)(C)[C@@H]1CCC(N)=O)OP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=NC2=C1N=C(N)NC2=O InChI=1S/C58H86N16O18P2.C10H12N5O3.Co/c1-25(91-94(87,88)92-93(85,86)89-23-33-45(82)46(83)52(90-33)74-24-67-44-50(74)71-53(65)72-51(44)84)22-66-41(81)16-17-55(6)31(18-38(62)78)49-58(9)57(8,21-40(64)80)30(12-15-37(61)77)43(73-58)27(3)48-56(7,20-39(63)79)28(10-13-35(59)75)32(68-48)19-34-54(4,5)29(11-14-36(60)76)42(69-34)26(2)47(55)70-49;1-4-6(16)7(17)10(18-4)15-3-14-5-8(11)12-2-13-9(5)15;/h19,24-25,28-31,33,45-46,49,52,82-83H,10-18,20-23H2,1-9H3,(H19,59,60,61,62,63,64,65,66,68,69,70,71,72,73,75,76,77,78,79,80,81,84,85,86,87,88);2-4,6-7,10,16-17H,1H2,(H2,11,12,13);/q;;+2/p-1/t25?,28-,29-,30-,31+,33-,45-,46-,49?,52-,55-,56+,57+,58+;4-,6-,7-,10-;/m11./s1 IQTYKHRKNGVJEO-FGHWVWCISA-M Solid Cytosol Membrane logp 0.07 ALOGPS logs -4.74 ALOGPS solubility 3.33e-02 g/l ALOGPS logp -16 ChemAxon pka_strongest_acidic 1.85 ChemAxon pka_strongest_basic 4.01 ChemAxon iupac (3R,4S,5S,9S,10S,15S,19R,20R,21R)-19-(2-{[(2R)-2-({[({[(2R,3S,4R,5R)-5-(2-amino-6-oxo-6,9-dihydro-1H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)propyl]carbamoyl}ethyl)-1-{[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl}-5,10,15-tris(2-carbamoylethyl)-4,9,20-tris(carbamoylmethyl)-3,4,7,9,14,14,17,19-octamethyl-2lambda5,22,23lambda5,24lambda5-tetraaza-1-cobaltaoctacyclo[11.9.1.1^{1,8}.0^{2,6}.0^{3,21}.0^{16,23}.0^{18,22}.0^{11,24}]tetracosa-2(6),7,11(24),12,16(23),17-hexaene-2,23,24-tris(ylium)-1,1-diuide ChemAxon average_mass 1665.5066 ChemAxon mono_mass 1664.597512489 ChemAxon smiles CC(CNC(=O)CC[C@]1(C)[C@@H](CC(N)=O)C2N=C1\C(C)=C1/N=C(/C=C3\N=C(\C(\C)=C4\[C@@H](CCC(N)=O)[C@](C)(CC(N)=O)[C@@]2(C)N4[Co+]C[C@H]2O[C@H]([C@H](O)[C@@H]2O)N2C=NC4=C2N=CN=C4N)[C@@](C)(CC(N)=O)[C@@H]3CCC(N)=O)C(C)(C)[C@@H]1CCC(N)=O)OP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=NC2=C1N=C(N)NC2=O ChemAxon formula C68H97CoN21O21P2 ChemAxon inchi InChI=1S/C58H86N16O18P2.C10H12N5O3.Co/c1-25(91-94(87,88)92-93(85,86)89-23-33-45(82)46(83)52(90-33)74-24-67-44-50(74)71-53(65)72-51(44)84)22-66-41(81)16-17-55(6)31(18-38(62)78)49-58(9)57(8,21-40(64)80)30(12-15-37(61)77)43(73-58)27(3)48-56(7,20-39(63)79)28(10-13-35(59)75)32(68-48)19-34-54(4,5)29(11-14-36(60)76)42(69-34)26(2)47(55)70-49;1-4-6(16)7(17)10(18-4)15-3-14-5-8(11)12-2-13-9(5)15;/h19,24-25,28-31,33,45-46,49,52,82-83H,10-18,20-23H2,1-9H3,(H19,59,60,61,62,63,64,65,66,68,69,70,71,72,73,75,76,77,78,79,80,81,84,85,86,87,88);2-4,6-7,10,16-17H,1H2,(H2,11,12,13);/q;;+2/p-1/t25?,28-,29-,30-,31+,33-,45-,46-,49?,52-,55-,56+,57+,58+;4-,6-,7-,10-;/m11./s1 ChemAxon inchikey IQTYKHRKNGVJEO-FGHWVWCISA-M ChemAxon polar_surface_area 656.5 ChemAxon refractivity 401.91 ChemAxon polarizability 161.78 ChemAxon rotatable_bond_count 31 ChemAxon acceptor_count 26 ChemAxon donor_count 16 ChemAxon physiological_charge -1 ChemAxon formal_charge 1 ChemAxon Porphyrin and chlorophyll metabolism ec00860 Metabolic pathways eco01100 adenosylcobalamin salvage from cobinamide Cobinamide is incorporated from the extracellular space through a transport system into the cytosol. Once inside the cytosol, cobinamide interacts with ATP through a cobinamide adenosyl transferase resulting in the release of a triphosphate and an adenosylcobinamide. The latter compound is then phosphorylated through an ATP-dependent cobinamide kinase resulting in the release of ADP, a hydrogen ion and adenosyl-cobinamide phosphate. This last compound then interacts with GTP and a hydrogen ion through a cobinamide-P guanylyltransferase resulting in the release of a pyrophosphate and an adenosylcobinamide-GDP. A dimethylbenzimidazole interacts with a nicotinate D-ribonucleotide through a nicotinate-nucleotide dimethylbenzumidazole phosphoribosyltransferase resulting in the release of a nicotinate, a hydrogen ion and an alpha-ribazole 5' phosphate. The adenosylcobinamide-GDP and the alpha-ribazole 5' phosphate interact together through a cobalamin 5' phosphate synthase resulting in the release of a hydrogen ion, a GMP and Adenosylcobalamin 5'-phosphate. The latter compound then interacts with a water molecule through an adenosylcbalamin 5' phosphate phosphatase resulting in the release of a phosphate and a coenzyme B12. Likewise a cobalamin molecule can interact with ATP through a cobalamin adenosyltransferase resulting in the release of a triphosphate and a coenzyme B12 PW001884 Metabolic adenosylcobalamin salvage from cobinamide I COBALSYN-PWY-1 Specdb::MsMs 3000292 Specdb::MsMs 3000293 Specdb::MsMs 3000294 HMDB12185 23724503 C06510 ADENOSYLCOBINAMIDE-GDP Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. 21097882 Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. 22080510 van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. 17765195 Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. 18331064 Bifunctional adenosylcobalamin biosynthesis protein cobU P0AE76 COBU_ECOLI cobU http://ecmdb.ca/proteins/P0AE76.xml Cobalamin synthase P36561 COBS_ECOLI cobS http://ecmdb.ca/proteins/P36561.xml Adenosylcobinamide-GDP + N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole > Adenosylcobalamin + Guanosine monophosphate + Hydrogen ion R05223 COBALAMINSYN-RXN Adenosyl cobinamide phosphate + Guanosine triphosphate + Hydrogen ion > Adenosylcobinamide-GDP + Pyrophosphate R05222 COBINPGUANYLYLTRANS-RXN Adenosyl cobinamide phosphate + Guanosine triphosphate <> Adenosylcobinamide-GDP + Pyrophosphate R05222 Adenosylcobalamin + Guanosine monophosphate <> Adenosylcobinamide-GDP + N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole R05223 Adenosylcobinamide-GDP + N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole > adenosylcobalamin 5'-phosphate + Guanosine monophosphate + Hydrogen ion COBALAMIN5PSYN-RXN Adenosylcobinamide-GDP + N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole Hydrogen ion + Adenosylcobalamin + Guanosine monophosphate COBALAMINSYN-RXN Guanosine triphosphate + adenosylcobinamide phosphate > Pyrophosphate + Adenosylcobinamide-GDP Adenosylcobinamide-GDP + N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole + N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole <> Guanosine monophosphate + Adenosylcobalamin + Adenosylcobalamin 5'-phosphate R05223 adenosylcobinamide phosphate + Guanosine triphosphate + Hydrogen ion > Pyrophosphate + Adenosylcobinamide-GDP + Adenosylcobinamide-GDP PW_R005141 N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole + Adenosylcobinamide-GDP + Adenosylcobinamide-GDP > Hydrogen ion + GMP + Adenosylcobalamin 5'-phosphate PW_R005143 Adenosyl cobinamide phosphate + Guanosine triphosphate + Hydrogen ion > Adenosylcobinamide-GDP + Pyrophosphate